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- PDB-7s46: PAK4cat (D440N/S474E) in complex with Integrin beta5 760-770 peptide -

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Basic information

Entry
Database: PDB / ID: 7s46
TitlePAK4cat (D440N/S474E) in complex with Integrin beta5 760-770 peptide
Components
  • Integrin beta-5
  • Isoform 2 of Serine/threonine-protein kinase PAK 4
KeywordsTRANSFERASE / serine/threonine kinase
Function / homology
Function and homology information


integrin alphav-beta5 complex / epithelial cell-cell adhesion / Cross-presentation of particulate exogenous antigens (phagosomes) / dendritic spine development / cadherin binding involved in cell-cell adhesion / Activation of RAC1 / wound healing, spreading of epidermal cells / integrin complex / Molecules associated with elastic fibres / cell adhesion mediated by integrin ...integrin alphav-beta5 complex / epithelial cell-cell adhesion / Cross-presentation of particulate exogenous antigens (phagosomes) / dendritic spine development / cadherin binding involved in cell-cell adhesion / Activation of RAC1 / wound healing, spreading of epidermal cells / integrin complex / Molecules associated with elastic fibres / cell adhesion mediated by integrin / RHOV GTPase cycle / Syndecan interactions / stress fiber assembly / RHOJ GTPase cycle / endodermal cell differentiation / RHOQ GTPase cycle / : / TGF-beta receptor signaling activates SMADs / regulation of MAPK cascade / RHOU GTPase cycle / CDC42 GTPase cycle / RHOH GTPase cycle / RHOG GTPase cycle / Smooth Muscle Contraction / RAC2 GTPase cycle / ECM proteoglycans / RAC3 GTPase cycle / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / phagocytic vesicle / cytoskeleton organization / RAC1 GTPase cycle / transforming growth factor beta receptor signaling pathway / cellular response to starvation / cell-matrix adhesion / integrin-mediated signaling pathway / adherens junction / regulation of cell growth / cell-cell adhesion / positive regulation of angiogenesis / integrin binding / cell migration / virus receptor activity / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / receptor complex / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / apoptotic process / cell surface / Golgi apparatus / signal transduction / extracellular exosome / ATP binding / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain ...p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain / Integrin EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrins beta chain EGF (I-EGF) domain profile. / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain EGF (I-EGF) domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / Integrin domain superfamily / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / Protein kinase domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Serine/threonine-protein kinase PAK 4 / Integrin beta-5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHa, B.H. / Boggon, T.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM138411 United States
CitationJournal: Commun Biol / Year: 2022
Title: Molecular basis for integrin adhesion receptor binding to p21-activated kinase 4 (PAK4)
Authors: Ha, B.H. / Yigit, S. / Natarajan, N. / Morse, E.M. / Calderwood, D.A. / Boggon, T.J.
History
DepositionSep 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 2 of Serine/threonine-protein kinase PAK 4
B: Integrin beta-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9493
Polymers40,4432
Non-polymers5061
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-5 kcal/mol
Surface area13690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.821, 61.821, 178.829
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Isoform 2 of Serine/threonine-protein kinase PAK 4 / p21-activated kinase 4 / PAK-4


Mass: 39084.203 Da / Num. of mol.: 1 / Mutation: D440N, S474E
Source method: isolated from a genetically manipulated source
Details: PAK4 catalytic domain (109-426) with D440N, S474E mutation
Source: (gene. exp.) Homo sapiens (human) / Gene: PAK4, KIAA1142 / Production host: Escherichia coli (E. coli)
References: UniProt: O96013, non-specific serine/threonine protein kinase
#2: Protein/peptide Integrin beta-5


Mass: 1358.505 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthetic peptide of Integrin beta 5 cytosolic domain (760-Glu-Arg-Ser-Arg-Ala-Arg-Tyr-Glu-Met-Ala-Ser-770)
Source: (synth.) Homo sapiens (human) / References: UniProt: P18084
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl (pH 8.5) and 0.5 M tri-sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.1→50.01 Å / Num. obs: 21249 / % possible obs: 99.9 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.04 / Rrim(I) all: 0.138 / Χ2: 0.682 / Net I/σ(I): 5.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.189.31.34320630.4470.4571.4210.451100
2.18-2.2612.11.15920720.6850.3461.210.453100
2.26-2.3712.60.8620900.8120.2520.8970.472100
2.37-2.4912.10.69420740.9050.2070.7240.489100
2.49-2.6511.90.49220730.9360.1480.5140.53399.8
2.65-2.8511.20.32621000.9670.1010.3420.639100
2.85-3.149.60.19921170.9860.0670.2110.847100
3.14-3.5912.80.13221380.9930.0380.1380.975100
3.59-4.5212.40.08521810.9970.0250.0890.94999.9
4.52-5010.50.05323410.9990.0170.0560.94699.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0151refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FIF

4fif


Resolution: 2.1→50.01 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / SU B: 12.257 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.187 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2197 1033 4.9 %RANDOM
Rwork0.1802 ---
obs0.1822 20098 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 122.53 Å2 / Biso mean: 47.78 Å2 / Biso min: 29.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å20 Å20 Å2
2---0.87 Å20 Å2
3---1.75 Å2
Refinement stepCycle: final / Resolution: 2.1→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2367 0 10 67 2444
Biso mean--55.5 46.02 -
Num. residues----299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192426
X-RAY DIFFRACTIONr_bond_other_d0.0020.022405
X-RAY DIFFRACTIONr_angle_refined_deg1.8321.9853282
X-RAY DIFFRACTIONr_angle_other_deg1.02835526
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.115297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26223.208106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54915438
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3731522
X-RAY DIFFRACTIONr_chiral_restr0.1020.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212691
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02541
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 79 -
Rwork0.307 1438 -
all-1517 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -21.0674 Å / Origin y: 11.4897 Å / Origin z: -6.7828 Å
111213212223313233
T0.0507 Å2-0.0385 Å20.0453 Å2-0.0364 Å2-0.0315 Å2--0.0505 Å2
L1.5527 °20.2107 °2-0.222 °2-0.9258 °2-0.6652 °2--1.6281 °2
S0.1338 Å °-0.1588 Å °0.0296 Å °0.0727 Å °-0.1045 Å °0.0536 Å °0.0031 Å °0.0843 Å °-0.0293 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A300 - 306
2X-RAY DIFFRACTION1A307 - 345
3X-RAY DIFFRACTION1A346 - 360
4X-RAY DIFFRACTION1A361 - 374
5X-RAY DIFFRACTION1A375 - 381
6X-RAY DIFFRACTION1A382 - 410
7X-RAY DIFFRACTION1A411 - 433
8X-RAY DIFFRACTION1A434 - 472
9X-RAY DIFFRACTION1A473 - 525
10X-RAY DIFFRACTION1A526 - 538
11X-RAY DIFFRACTION1A539 - 567
12X-RAY DIFFRACTION1A568 - 589

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